Small fix

Reviewed-on: #2

config/app_config.yaml

@@ -12,12 +12,28 @@ image_repository:
 models:
   default_base_model: yolov8s-seg.pt
   models_directory: data/models
+  base_model_choices:
+  - yolov8s-seg.pt
+  - yolo11s-seg.pt
 training:
   default_epochs: 100
   default_batch_size: 16
-  default_imgsz: 640
+  default_imgsz: 1024
   default_patience: 50
   default_lr0: 0.01
+  two_stage:
+    enabled: false
+    stage1:
+      epochs: 20
+      lr0: 0.0005
+      patience: 10
+      freeze: 10
+    stage2:
+      epochs: 150
+      lr0: 0.0003
+      patience: 30
+  last_dataset_yaml: /home/martin/code/object_detection/data/datasets/data.yaml
+  last_dataset_dir: /home/martin/code/object_detection/data/datasets
 detection:
   default_confidence: 0.25
   default_iou: 0.45

src/database/db_manager.py

@@ -10,6 +10,14 @@ from typing import List, Dict, Optional, Tuple, Any, Union
 from pathlib import Path
 import csv
 import hashlib
+import yaml
+
+from src.utils.logger import get_logger
+from src.utils.image import Image
+
+IMAGE_EXTENSIONS = tuple(Image.SUPPORTED_EXTENSIONS)
+
+logger = get_logger(__name__)
 
 
 class DatabaseManager:
@@ -443,6 +451,25 @@ class DatabaseManager:
             filters["model_id"] = model_id
         return self.get_detections(filters)
 
+    def delete_detections_for_image(
+        self, image_id: int, model_id: Optional[int] = None
+    ) -> int:
+        """Delete detections tied to a specific image and optional model."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            if model_id is not None:
+                cursor.execute(
+                    "DELETE FROM detections WHERE image_id = ? AND model_id = ?",
+                    (image_id, model_id),
+                )
+            else:
+                cursor.execute("DELETE FROM detections WHERE image_id = ?", (image_id,))
+            conn.commit()
+            return cursor.rowcount
+        finally:
+            conn.close()
+
     def delete_detections_for_model(self, model_id: int) -> int:
         """Delete all detections for a specific model."""
         conn = self.get_connection()
@@ -861,6 +888,187 @@ class DatabaseManager:
         finally:
             conn.close()
 
+    # ==================== Dataset Utilities ====================
+
+    def compose_data_yaml(
+        self,
+        dataset_root: str,
+        output_path: Optional[str] = None,
+        splits: Optional[Dict[str, str]] = None,
+    ) -> str:
+        """
+        Compose a YOLO data.yaml file based on dataset folders and database metadata.
+
+        Args:
+            dataset_root: Base directory containing the dataset structure.
+            output_path: Optional output path; defaults to <dataset_root>/data.yaml.
+            splits: Optional mapping overriding train/val/test image directories (relative
+                to dataset_root or absolute paths).
+
+        Returns:
+            Path to the generated YAML file.
+        """
+        dataset_root_path = Path(dataset_root).expanduser()
+        if not dataset_root_path.exists():
+            raise ValueError(f"Dataset root does not exist: {dataset_root_path}")
+        dataset_root_path = dataset_root_path.resolve()
+
+        split_map: Dict[str, str] = {key: "" for key in ("train", "val", "test")}
+        if splits:
+            for key, value in splits.items():
+                if key in split_map and value:
+                    split_map[key] = value
+
+        inferred = self._infer_split_dirs(dataset_root_path)
+        for key in split_map:
+            if not split_map[key]:
+                split_map[key] = inferred.get(key, "")
+
+        for required in ("train", "val"):
+            if not split_map[required]:
+                raise ValueError(
+                    "Unable to determine %s image directory under %s. Provide it "
+                    "explicitly via the 'splits' argument."
+                    % (required, dataset_root_path)
+                )
+
+        yaml_splits: Dict[str, str] = {}
+        for key, value in split_map.items():
+            if not value:
+                continue
+            yaml_splits[key] = self._normalize_split_value(value, dataset_root_path)
+
+        class_names = self._fetch_annotation_class_names()
+        if not class_names:
+            class_names = [cls["class_name"] for cls in self.get_object_classes()]
+        if not class_names:
+            raise ValueError("No object classes available to populate data.yaml")
+
+        names_map = {idx: name for idx, name in enumerate(class_names)}
+        payload: Dict[str, Any] = {
+            "path": dataset_root_path.as_posix(),
+            "train": yaml_splits["train"],
+            "val": yaml_splits["val"],
+            "names": names_map,
+            "nc": len(class_names),
+        }
+        if yaml_splits.get("test"):
+            payload["test"] = yaml_splits["test"]
+
+        output_path_obj = (
+            Path(output_path).expanduser()
+            if output_path
+            else dataset_root_path / "data.yaml"
+        )
+        output_path_obj.parent.mkdir(parents=True, exist_ok=True)
+
+        with open(output_path_obj, "w", encoding="utf-8") as handle:
+            yaml.safe_dump(payload, handle, sort_keys=False)
+
+        logger.info(f"Generated data.yaml at {output_path_obj}")
+        return output_path_obj.as_posix()
+
+    def _fetch_annotation_class_names(self) -> List[str]:
+        """Return class names referenced by annotations (ordered by class ID)."""
+        conn = self.get_connection()
+        try:
+            cursor = conn.cursor()
+            cursor.execute(
+                """
+                SELECT DISTINCT c.id, c.class_name
+                FROM annotations a
+                JOIN object_classes c ON a.class_id = c.id
+                ORDER BY c.id
+                """
+            )
+            rows = cursor.fetchall()
+            return [row["class_name"] for row in rows]
+        finally:
+            conn.close()
+
+    def _infer_split_dirs(self, dataset_root: Path) -> Dict[str, str]:
+        """Infer train/val/test image directories relative to dataset_root."""
+        patterns = {
+            "train": [
+                "train/images",
+                "training/images",
+                "images/train",
+                "images/training",
+                "train",
+                "training",
+            ],
+            "val": [
+                "val/images",
+                "validation/images",
+                "images/val",
+                "images/validation",
+                "val",
+                "validation",
+            ],
+            "test": [
+                "test/images",
+                "testing/images",
+                "images/test",
+                "images/testing",
+                "test",
+                "testing",
+            ],
+        }
+
+        inferred: Dict[str, str] = {key: "" for key in patterns}
+        for split_name, options in patterns.items():
+            for relative in options:
+                candidate = (dataset_root / relative).resolve()
+                if (
+                    candidate.exists()
+                    and candidate.is_dir()
+                    and self._directory_has_images(candidate)
+                ):
+                    try:
+                        inferred[split_name] = candidate.relative_to(
+                            dataset_root
+                        ).as_posix()
+                    except ValueError:
+                        inferred[split_name] = candidate.as_posix()
+                    break
+        return inferred
+
+    def _normalize_split_value(self, split_value: str, dataset_root: Path) -> str:
+        """Validate and normalize a split directory to a YAML-friendly string."""
+        split_path = Path(split_value).expanduser()
+        if not split_path.is_absolute():
+            split_path = (dataset_root / split_path).resolve()
+        else:
+            split_path = split_path.resolve()
+
+        if not split_path.exists() or not split_path.is_dir():
+            raise ValueError(f"Split directory not found: {split_path}")
+
+        if not self._directory_has_images(split_path):
+            raise ValueError(f"No images found under {split_path}")
+
+        try:
+            return split_path.relative_to(dataset_root).as_posix()
+        except ValueError:
+            return split_path.as_posix()
+
+    @staticmethod
+    def _directory_has_images(directory: Path, max_checks: int = 2000) -> bool:
+        """Return True if directory tree contains at least one image file."""
+        checked = 0
+        try:
+            for file_path in directory.rglob("*"):
+                if not file_path.is_file():
+                    continue
+                if file_path.suffix.lower() in IMAGE_EXTENSIONS:
+                    return True
+                checked += 1
+                if checked >= max_checks:
+                    break
+        except Exception:
+            return False
+        return False
+
     @staticmethod
     def calculate_checksum(file_path: str) -> str:
         """Calculate MD5 checksum of a file."""

src/gui/main_window.py

@@ -297,7 +297,9 @@ class MainWindow(QMainWindow):
             # Save window state before closing
             self._save_window_state()
 
-            # Save annotation tab state if it exists
+            # Persist tab state and stop background work before exit
+            if hasattr(self, "training_tab"):
+                self.training_tab.shutdown()
             if hasattr(self, "annotation_tab"):
                 self.annotation_tab.save_state()
 

src/gui/tabs/annotation_tab.py

@@ -168,7 +168,7 @@ class AnnotationTab(QWidget):
             self,
             "Select Image",
             start_dir,
-            "Images (*.jpg *.jpeg *.png *.tif *.tiff *.bmp)",
+            "Images (*" + " *".join(Image.SUPPORTED_EXTENSIONS) + ")",
         )
 
         if not file_path:

src/gui/tabs/detection_tab.py

@@ -20,12 +20,14 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import Qt, QThread, Signal
 from pathlib import Path
+from typing import Optional
 
 from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
 from src.utils.logger import get_logger
 from src.utils.file_utils import get_image_files
 from src.model.inference import InferenceEngine
+from src.utils.image import Image
 
 
 logger = get_logger(__name__)
@@ -147,29 +149,65 @@ class DetectionTab(QWidget):
         self.model_combo.currentIndexChanged.connect(self._on_model_changed)
 
     def _load_models(self):
-        """Load available models from database."""
+        """Load available models from database and local storage."""
         try:
-            models = self.db_manager.get_models()
             self.model_combo.clear()
+            models = self.db_manager.get_models()
+            has_models = False
 
-            if not models:
-                self.model_combo.addItem("No models available", None)
-                self._set_buttons_enabled(False)
-                return
+            known_paths = set()
 
-            # Add base model option
+            # Add base model option first (always available)
             base_model = self.config_manager.get(
                 "models.default_base_model", "yolov8s-seg.pt"
             )
-            self.model_combo.addItem(
-                f"Base Model ({base_model})", {"id": 0, "path": base_model}
-            )
+            if base_model:
+                base_data = {
+                    "id": 0,
+                    "path": base_model,
+                    "model_name": Path(base_model).stem or "Base Model",
+                    "model_version": "pretrained",
+                    "base_model": base_model,
+                    "source": "base",
+                }
+                self.model_combo.addItem(f"Base Model ({base_model})", base_data)
+                known_paths.add(self._normalize_model_path(base_model))
+                has_models = True
 
-            # Add trained models
+            # Add trained models from database
             for model in models:
                 display_name = f"{model['model_name']} v{model['model_version']}"
-                self.model_combo.addItem(display_name, model)
+                model_data = {**model, "path": model.get("model_path")}
+                normalized = self._normalize_model_path(model_data.get("path"))
+                if normalized:
+                    known_paths.add(normalized)
+                self.model_combo.addItem(display_name, model_data)
+                has_models = True
 
+            # Discover local model files not yet in the database
+            local_models = self._discover_local_models()
+            for model_path in local_models:
+                normalized = self._normalize_model_path(model_path)
+                if normalized in known_paths:
+                    continue
+
+                display_name = f"Local Model ({Path(model_path).stem})"
+                model_data = {
+                    "id": None,
+                    "path": str(model_path),
+                    "model_name": Path(model_path).stem,
+                    "model_version": "local",
+                    "base_model": Path(model_path).stem,
+                    "source": "local",
+                }
+                self.model_combo.addItem(display_name, model_data)
+                known_paths.add(normalized)
+                has_models = True
+
+            if not has_models:
+                self.model_combo.addItem("No models available", None)
+                self._set_buttons_enabled(False)
+            else:
                 self._set_buttons_enabled(True)
 
         except Exception as e:
@@ -199,7 +237,7 @@ class DetectionTab(QWidget):
             self,
             "Select Image",
             start_dir,
-            "Images (*.jpg *.jpeg *.png *.tif *.tiff *.bmp)",
+            "Images (*" + " *".join(Image.SUPPORTED_EXTENSIONS) + ")",
         )
 
         if not file_path:
@@ -249,25 +287,39 @@ class DetectionTab(QWidget):
                 QMessageBox.warning(self, "No Model", "Please select a model first.")
                 return
 
-            model_path = model_data["path"]
-            model_id = model_data["id"]
+            model_path = model_data.get("path")
+            if not model_path:
+                QMessageBox.warning(
+                    self, "Invalid Model", "Selected model is missing a file path."
+                )
+                return
 
-            # Ensure we have a valid model ID (create entry for base model if needed)
-            if model_id == 0:
-                # Create database entry for base model
-                base_model = self.config_manager.get(
-                    "models.default_base_model", "yolov8s-seg.pt"
+            if not Path(model_path).exists():
+                QMessageBox.critical(
+                    self,
+                    "Model Not Found",
+                    f"The selected model file could not be found:\n{model_path}",
                 )
-                model_id = self.db_manager.add_model(
-                    model_name="Base Model",
-                    model_version="pretrained",
-                    model_path=base_model,
-                    base_model=base_model,
+                return
+
+            model_id = model_data.get("id")
+
+            # Ensure we have a database entry for the selected model
+            if model_id in (None, 0):
+                model_id = self._ensure_model_record(model_data)
+                if not model_id:
+                    QMessageBox.critical(
+                        self,
+                        "Model Registration Failed",
+                        "Unable to register the selected model in the database.",
                     )
+                    return
+
+            normalized_model_path = self._normalize_model_path(model_path) or model_path
 
             # Create inference engine
             self.inference_engine = InferenceEngine(
-                model_path, self.db_manager, model_id
+                normalized_model_path, self.db_manager, model_id
             )
 
             # Get confidence threshold
@@ -338,6 +390,76 @@ class DetectionTab(QWidget):
         self.batch_btn.setEnabled(enabled)
         self.model_combo.setEnabled(enabled)
 
+    def _discover_local_models(self) -> list:
+        """Scan the models directory for standalone .pt files."""
+        models_dir = self.config_manager.get_models_directory()
+        if not models_dir:
+            return []
+
+        models_path = Path(models_dir)
+        if not models_path.exists():
+            return []
+
+        try:
+            return sorted(
+                [p for p in models_path.rglob("*.pt") if p.is_file()],
+                key=lambda p: str(p).lower(),
+            )
+        except Exception as e:
+            logger.warning(f"Error discovering local models: {e}")
+            return []
+
+    def _normalize_model_path(self, path_value) -> str:
+        """Return a normalized absolute path string for comparison."""
+        if not path_value:
+            return ""
+        try:
+            return str(Path(path_value).resolve())
+        except Exception:
+            return str(path_value)
+
+    def _ensure_model_record(self, model_data: dict) -> Optional[int]:
+        """Ensure a database record exists for the selected model."""
+        model_path = model_data.get("path")
+        if not model_path:
+            return None
+
+        normalized_target = self._normalize_model_path(model_path)
+
+        try:
+            existing_models = self.db_manager.get_models()
+            for model in existing_models:
+                existing_path = model.get("model_path")
+                if not existing_path:
+                    continue
+                normalized_existing = self._normalize_model_path(existing_path)
+                if (
+                    normalized_existing == normalized_target
+                    or existing_path == model_path
+                ):
+                    return model["id"]
+
+            model_name = (
+                model_data.get("model_name") or Path(model_path).stem or "Custom Model"
+            )
+            model_version = (
+                model_data.get("model_version") or model_data.get("source") or "local"
+            )
+            base_model = model_data.get(
+                "base_model",
+                self.config_manager.get("models.default_base_model", "yolov8s-seg.pt"),
+            )
+
+            return self.db_manager.add_model(
+                model_name=model_name,
+                model_version=model_version,
+                model_path=normalized_target,
+                base_model=base_model,
+            )
+        except Exception as e:
+            logger.error(f"Failed to ensure model record for {model_path}: {e}")
+            return None
+
     def refresh(self):
         """Refresh the tab."""
         self._load_models()

src/gui/tabs/results_tab.py

@@ -1,15 +1,39 @@
 """
-Results tab for the microscopy object detection application.
+Results tab for browsing stored detections and visualizing overlays.
 """
 
-from PySide6.QtWidgets import QWidget, QVBoxLayout, QLabel, QGroupBox
+from pathlib import Path
+from typing import Dict, List, Optional
+
+from PySide6.QtWidgets import (
+    QWidget,
+    QVBoxLayout,
+    QHBoxLayout,
+    QLabel,
+    QGroupBox,
+    QPushButton,
+    QSplitter,
+    QTableWidget,
+    QTableWidgetItem,
+    QHeaderView,
+    QAbstractItemView,
+    QMessageBox,
+    QCheckBox,
+)
+from PySide6.QtCore import Qt
 
 from src.database.db_manager import DatabaseManager
 from src.utils.config_manager import ConfigManager
+from src.utils.logger import get_logger
+from src.utils.image import Image, ImageLoadError
+from src.gui.widgets import AnnotationCanvasWidget
+
+
+logger = get_logger(__name__)
 
 
 class ResultsTab(QWidget):
-    """Results tab placeholder."""
+    """Results tab showing detection history and preview overlays."""
 
     def __init__(
         self, db_manager: DatabaseManager, config_manager: ConfigManager, parent=None
@@ -18,29 +42,398 @@ class ResultsTab(QWidget):
         self.db_manager = db_manager
         self.config_manager = config_manager
 
+        self.detection_summary: List[Dict] = []
+        self.current_selection: Optional[Dict] = None
+        self.current_image: Optional[Image] = None
+        self.current_detections: List[Dict] = []
+        self._image_path_cache: Dict[str, str] = {}
+
         self._setup_ui()
+        self.refresh()
 
     def _setup_ui(self):
         """Setup user interface."""
         layout = QVBoxLayout()
 
-        group = QGroupBox("Results")
-        group_layout = QVBoxLayout()
-        label = QLabel(
-            "Results viewer will be implemented here.\n\n"
-            "Features:\n"
-            "- Detection history browser\n"
-            "- Advanced filtering\n"
-            "- Statistics dashboard\n"
-            "- Export functionality"
-        )
-        group_layout.addWidget(label)
-        group.setLayout(group_layout)
+        # Splitter for list + preview
+        splitter = QSplitter(Qt.Horizontal)
 
-        layout.addWidget(group)
-        layout.addStretch()
+        # Left pane: detection list
+        left_container = QWidget()
+        left_layout = QVBoxLayout()
+        left_layout.setContentsMargins(0, 0, 0, 0)
+
+        controls_layout = QHBoxLayout()
+        self.refresh_btn = QPushButton("Refresh")
+        self.refresh_btn.clicked.connect(self.refresh)
+        controls_layout.addWidget(self.refresh_btn)
+        controls_layout.addStretch()
+        left_layout.addLayout(controls_layout)
+
+        self.results_table = QTableWidget(0, 5)
+        self.results_table.setHorizontalHeaderLabels(
+            ["Image", "Model", "Detections", "Classes", "Last Updated"]
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            0, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            1, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            2, QHeaderView.ResizeToContents
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            3, QHeaderView.Stretch
+        )
+        self.results_table.horizontalHeader().setSectionResizeMode(
+            4, QHeaderView.ResizeToContents
+        )
+        self.results_table.setSelectionBehavior(QAbstractItemView.SelectRows)
+        self.results_table.setSelectionMode(QAbstractItemView.SingleSelection)
+        self.results_table.setEditTriggers(QAbstractItemView.NoEditTriggers)
+        self.results_table.itemSelectionChanged.connect(self._on_result_selected)
+
+        left_layout.addWidget(self.results_table)
+        left_container.setLayout(left_layout)
+
+        # Right pane: preview canvas and controls
+        right_container = QWidget()
+        right_layout = QVBoxLayout()
+        right_layout.setContentsMargins(0, 0, 0, 0)
+
+        preview_group = QGroupBox("Detection Preview")
+        preview_layout = QVBoxLayout()
+
+        self.preview_canvas = AnnotationCanvasWidget()
+        self.preview_canvas.set_polyline_enabled(False)
+        self.preview_canvas.set_show_bboxes(True)
+        preview_layout.addWidget(self.preview_canvas)
+
+        toggles_layout = QHBoxLayout()
+        self.show_masks_checkbox = QCheckBox("Show Masks")
+        self.show_masks_checkbox.setChecked(False)
+        self.show_masks_checkbox.stateChanged.connect(self._apply_detection_overlays)
+        self.show_bboxes_checkbox = QCheckBox("Show Bounding Boxes")
+        self.show_bboxes_checkbox.setChecked(True)
+        self.show_bboxes_checkbox.stateChanged.connect(self._toggle_bboxes)
+        self.show_confidence_checkbox = QCheckBox("Show Confidence")
+        self.show_confidence_checkbox.setChecked(False)
+        self.show_confidence_checkbox.stateChanged.connect(
+            self._apply_detection_overlays
+        )
+        toggles_layout.addWidget(self.show_masks_checkbox)
+        toggles_layout.addWidget(self.show_bboxes_checkbox)
+        toggles_layout.addWidget(self.show_confidence_checkbox)
+        toggles_layout.addStretch()
+        preview_layout.addLayout(toggles_layout)
+
+        self.summary_label = QLabel("Select a detection result to preview.")
+        self.summary_label.setWordWrap(True)
+        preview_layout.addWidget(self.summary_label)
+
+        preview_group.setLayout(preview_layout)
+        right_layout.addWidget(preview_group)
+        right_container.setLayout(right_layout)
+
+        splitter.addWidget(left_container)
+        splitter.addWidget(right_container)
+        splitter.setStretchFactor(0, 1)
+        splitter.setStretchFactor(1, 2)
+
+        layout.addWidget(splitter)
         self.setLayout(layout)
 
     def refresh(self):
-        """Refresh the tab."""
-        pass
+        """Refresh the detection list and preview."""
+        self._load_detection_summary()
+        self._populate_results_table()
+        self.current_selection = None
+        self.current_image = None
+        self.current_detections = []
+        self.preview_canvas.clear()
+        self.summary_label.setText("Select a detection result to preview.")
+
+    def _load_detection_summary(self):
+        """Load latest detection summaries grouped by image + model."""
+        try:
+            detections = self.db_manager.get_detections(limit=500)
+            summary_map: Dict[tuple, Dict] = {}
+
+            for det in detections:
+                key = (det["image_id"], det["model_id"])
+                metadata = det.get("metadata") or {}
+                entry = summary_map.setdefault(
+                    key,
+                    {
+                        "image_id": det["image_id"],
+                        "model_id": det["model_id"],
+                        "image_path": det.get("image_path"),
+                        "image_filename": det.get("image_filename")
+                        or det.get("image_path"),
+                        "model_name": det.get("model_name", ""),
+                        "model_version": det.get("model_version", ""),
+                        "last_detected": det.get("detected_at"),
+                        "count": 0,
+                        "classes": set(),
+                        "source_path": metadata.get("source_path"),
+                        "repository_root": metadata.get("repository_root"),
+                    },
+                )
+
+                entry["count"] += 1
+                if det.get("detected_at") and (
+                    not entry.get("last_detected")
+                    or str(det.get("detected_at")) > str(entry.get("last_detected"))
+                ):
+                    entry["last_detected"] = det.get("detected_at")
+                if det.get("class_name"):
+                    entry["classes"].add(det["class_name"])
+                if metadata.get("source_path") and not entry.get("source_path"):
+                    entry["source_path"] = metadata.get("source_path")
+                if metadata.get("repository_root") and not entry.get("repository_root"):
+                    entry["repository_root"] = metadata.get("repository_root")
+
+            self.detection_summary = sorted(
+                summary_map.values(),
+                key=lambda x: str(x.get("last_detected") or ""),
+                reverse=True,
+            )
+        except Exception as e:
+            logger.error(f"Failed to load detection summary: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load detection results:\n{str(e)}",
+            )
+            self.detection_summary = []
+
+    def _populate_results_table(self):
+        """Populate the table widget with detection summaries."""
+        self.results_table.setRowCount(len(self.detection_summary))
+
+        for row, entry in enumerate(self.detection_summary):
+            model_label = f"{entry['model_name']} {entry['model_version']}".strip()
+            class_list = (
+                ", ".join(sorted(entry["classes"])) if entry["classes"] else "-"
+            )
+
+            items = [
+                QTableWidgetItem(entry.get("image_filename", "")),
+                QTableWidgetItem(model_label),
+                QTableWidgetItem(str(entry.get("count", 0))),
+                QTableWidgetItem(class_list),
+                QTableWidgetItem(str(entry.get("last_detected") or "")),
+            ]
+
+            for col, item in enumerate(items):
+                item.setData(Qt.UserRole, row)
+                self.results_table.setItem(row, col, item)
+
+        self.results_table.clearSelection()
+
+    def _on_result_selected(self):
+        """Handle selection changes in the detection table."""
+        selected_items = self.results_table.selectedItems()
+        if not selected_items:
+            return
+
+        row = selected_items[0].data(Qt.UserRole)
+        if row is None or row >= len(self.detection_summary):
+            return
+
+        entry = self.detection_summary[row]
+        if (
+            self.current_selection
+            and self.current_selection.get("image_id") == entry["image_id"]
+            and self.current_selection.get("model_id") == entry["model_id"]
+        ):
+            return
+
+        self.current_selection = entry
+
+        image_path = self._resolve_image_path(entry)
+        if not image_path:
+            QMessageBox.warning(
+                self,
+                "Image Not Found",
+                "Unable to locate the image file for this detection.",
+            )
+            return
+
+        try:
+            self.current_image = Image(image_path)
+            self.preview_canvas.load_image(self.current_image)
+        except ImageLoadError as e:
+            logger.error(f"Failed to load image '{image_path}': {e}")
+            QMessageBox.critical(
+                self,
+                "Image Error",
+                f"Failed to load image for preview:\n{str(e)}",
+            )
+            return
+
+        self._load_detections_for_selection(entry)
+        self._apply_detection_overlays()
+        self._update_summary_label(entry)
+
+    def _load_detections_for_selection(self, entry: Dict):
+        """Load detection records for the selected image/model pair."""
+        self.current_detections = []
+        if not entry:
+            return
+
+        try:
+            filters = {"image_id": entry["image_id"], "model_id": entry["model_id"]}
+            self.current_detections = self.db_manager.get_detections(filters)
+        except Exception as e:
+            logger.error(f"Failed to load detections for preview: {e}")
+            QMessageBox.critical(
+                self,
+                "Error",
+                f"Failed to load detections for this image:\n{str(e)}",
+            )
+            self.current_detections = []
+
+    def _apply_detection_overlays(self):
+        """Draw detections onto the preview canvas based on current toggles."""
+        self.preview_canvas.clear_annotations()
+        self.preview_canvas.set_show_bboxes(self.show_bboxes_checkbox.isChecked())
+
+        if not self.current_detections or not self.current_image:
+            return
+
+        for det in self.current_detections:
+            color = self._get_class_color(det.get("class_name"))
+
+            if self.show_masks_checkbox.isChecked() and det.get("segmentation_mask"):
+                mask_points = self._convert_mask(det["segmentation_mask"])
+                if mask_points:
+                    self.preview_canvas.draw_saved_polyline(mask_points, color)
+
+            bbox = [
+                det.get("x_min"),
+                det.get("y_min"),
+                det.get("x_max"),
+                det.get("y_max"),
+            ]
+            if all(v is not None for v in bbox):
+                label = None
+                if self.show_confidence_checkbox.isChecked():
+                    confidence = det.get("confidence")
+                    if confidence is not None:
+                        label = f"{confidence:.2f}"
+                self.preview_canvas.draw_saved_bbox(bbox, color, label=label)
+
+    def _convert_mask(self, mask_points: List[List[float]]) -> List[List[float]]:
+        """Convert stored [x, y] masks to [y, x] format for the canvas."""
+        converted = []
+        for point in mask_points:
+            if len(point) >= 2:
+                x, y = point[0], point[1]
+                converted.append([y, x])
+        return converted
+
+    def _toggle_bboxes(self):
+        """Update bounding box visibility on the canvas."""
+        self.preview_canvas.set_show_bboxes(self.show_bboxes_checkbox.isChecked())
+        # Re-render to respect show/hide when toggled
+        self._apply_detection_overlays()
+
+    def _update_summary_label(self, entry: Dict):
+        """Display textual summary for the selected detection run."""
+        classes = ", ".join(sorted(entry.get("classes", []))) or "-"
+        summary_text = (
+            f"Image: {entry.get('image_filename', 'unknown')}\n"
+            f"Model: {entry.get('model_name', '')} {entry.get('model_version', '')}\n"
+            f"Detections: {entry.get('count', 0)}\n"
+            f"Classes: {classes}\n"
+            f"Last Updated: {entry.get('last_detected', 'n/a')}"
+        )
+        self.summary_label.setText(summary_text)
+
+    def _resolve_image_path(self, entry: Dict) -> Optional[str]:
+        """Resolve an image path using metadata, cache, and repository hints."""
+        relative_path = entry.get("image_path") if entry else None
+        cache_key = relative_path or entry.get("source_path")
+        if cache_key and cache_key in self._image_path_cache:
+            cached = Path(self._image_path_cache[cache_key])
+            if cached.exists():
+                return self._image_path_cache[cache_key]
+            del self._image_path_cache[cache_key]
+
+        candidates = []
+        source_path = entry.get("source_path") if entry else None
+        if source_path:
+            candidates.append(Path(source_path))
+
+        repo_roots = []
+        if entry.get("repository_root"):
+            repo_roots.append(entry["repository_root"])
+        config_repo = self.config_manager.get_image_repository_path()
+        if config_repo:
+            repo_roots.append(config_repo)
+
+        for root in repo_roots:
+            if relative_path:
+                candidates.append(Path(root) / relative_path)
+
+        if relative_path:
+            candidates.append(Path(relative_path))
+
+        for candidate in candidates:
+            try:
+                if candidate and candidate.exists():
+                    resolved = str(candidate.resolve())
+                    if cache_key:
+                        self._image_path_cache[cache_key] = resolved
+                    return resolved
+            except Exception:
+                continue
+
+        # Fallback: search by filename in known roots
+        filename = Path(relative_path).name if relative_path else None
+        if filename:
+            search_roots = [Path(root) for root in repo_roots if root]
+            if not search_roots:
+                search_roots = [Path("data")]
+            match = self._search_in_roots(filename, search_roots)
+            if match:
+                resolved = str(match.resolve())
+                if cache_key:
+                    self._image_path_cache[cache_key] = resolved
+                return resolved
+
+        return None
+
+    def _search_in_roots(self, filename: str, roots: List[Path]) -> Optional[Path]:
+        """Search for a file name within a list of root directories."""
+        for root in roots:
+            try:
+                if not root.exists():
+                    continue
+                for candidate in root.rglob(filename):
+                    return candidate
+            except Exception as e:
+                logger.debug(f"Error searching for {filename} in {root}: {e}")
+        return None
+
+    def _get_class_color(self, class_name: Optional[str]) -> str:
+        """Return consistent color hex for a class name."""
+        if not class_name:
+            return "#FF6B6B"
+
+        color_map = self.config_manager.get_bbox_colors()
+        if class_name in color_map:
+            return color_map[class_name]
+
+        # Deterministic fallback color based on hash
+        palette = [
+            "#FF6B6B",
+            "#4ECDC4",
+            "#FFD166",
+            "#1D3557",
+            "#F4A261",
+            "#E76F51",
+        ]
+        return palette[hash(class_name) % len(palette)]

src/gui/widgets/annotation_canvas_widget.py

@@ -16,8 +16,9 @@ from PySide6.QtGui import (
     QKeyEvent,
     QMouseEvent,
     QPaintEvent,
+    QPolygonF,
 )
-from PySide6.QtCore import Qt, QEvent, Signal, QPoint
+from PySide6.QtCore import Qt, QEvent, Signal, QPoint, QPointF, QRect
 from typing import Any, Dict, List, Optional, Tuple
 
 from src.utils.image import Image, ImageLoadError
@@ -246,10 +247,10 @@ class AnnotationCanvasWidget(QWidget):
             return
 
         try:
-            # Get RGB image data
-            if self.current_image.channels == 3:
+            # Get image data in a format compatible with Qt
+            if self.current_image.channels in (3, 4):
                 image_data = self.current_image.get_rgb()
-                height, width, channels = image_data.shape
+                height, width = image_data.shape[:2]
             else:
                 image_data = self.current_image.get_grayscale()
                 height, width = image_data.shape
@@ -263,7 +264,7 @@ class AnnotationCanvasWidget(QWidget):
                 height,
                 bytes_per_line,
                 self.current_image.qtimage_format,
-            )
+            ).copy()  # Copy so Qt owns the buffer even after numpy array goes out of scope
 
             self.original_pixmap = QPixmap.fromImage(qimage)
 
@@ -496,8 +497,10 @@ class AnnotationCanvasWidget(QWidget):
                 )
 
             painter.setPen(pen)
-            for (x1, y1), (x2, y2) in zip(polyline[:-1], polyline[1:]):
-                painter.drawLine(int(x1), int(y1), int(x2), int(y2))
+            # Use QPolygonF for efficient polygon rendering (single call vs N-1 calls)
+            # drawPolygon() automatically closes the shape, ensuring proper visual closure
+            polygon = QPolygonF([QPointF(x, y) for x, y in polyline])
+            painter.drawPolygon(polygon)
 
         # Draw bounding boxes (dashed) if enabled
         if self.show_bboxes and self.original_pixmap is not None and self.bboxes:
@@ -529,6 +532,40 @@ class AnnotationCanvasWidget(QWidget):
                 painter.setPen(pen)
                 painter.drawRect(x_min, y_min, rect_width, rect_height)
 
+                label_text = meta.get("label")
+                if label_text:
+                    painter.save()
+                    font = painter.font()
+                    font.setPointSizeF(max(10.0, width + 4))
+                    painter.setFont(font)
+                    metrics = painter.fontMetrics()
+                    text_width = metrics.horizontalAdvance(label_text)
+                    text_height = metrics.height()
+                    padding = 4
+                    bg_width = text_width + padding * 2
+                    bg_height = text_height + padding * 2
+                    canvas_width = self.original_pixmap.width()
+                    canvas_height = self.original_pixmap.height()
+                    bg_x = max(0, min(x_min, canvas_width - bg_width))
+                    bg_y = y_min - bg_height
+                    if bg_y < 0:
+                        bg_y = min(y_min, canvas_height - bg_height)
+                        bg_y = max(0, bg_y)
+                    background_rect = QRect(bg_x, bg_y, bg_width, bg_height)
+                    background_color = QColor(pen_color)
+                    background_color.setAlpha(220)
+                    painter.fillRect(background_rect, background_color)
+                    text_color = QColor(0, 0, 0)
+                    if background_color.lightness() < 128:
+                        text_color = QColor(255, 255, 255)
+                    painter.setPen(text_color)
+                    painter.drawText(
+                        background_rect.adjusted(padding, padding, -padding, -padding),
+                        Qt.AlignLeft | Qt.AlignVCenter,
+                        label_text,
+                    )
+                    painter.restore()
+
         painter.end()
 
         self._update_display()
@@ -787,7 +824,13 @@ class AnnotationCanvasWidget(QWidget):
             f"Drew saved polyline with {len(polyline)} points in color {color}"
         )
 
-    def draw_saved_bbox(self, bbox: List[float], color: str, width: int = 3):
+    def draw_saved_bbox(
+        self,
+        bbox: List[float],
+        color: str,
+        width: int = 3,
+        label: Optional[str] = None,
+    ):
         """
         Draw a bounding box from database coordinates onto the annotation canvas.
 
@@ -796,6 +839,7 @@ class AnnotationCanvasWidget(QWidget):
                   in normalized coordinates (0-1)
             color: Color hex string (e.g., '#FF0000')
             width: Line width in pixels
+            label: Optional text label to render near the bounding box
         """
         if not self.annotation_pixmap or not self.original_pixmap:
             logger.warning("Cannot draw bounding box: no image loaded")
@@ -828,11 +872,11 @@ class AnnotationCanvasWidget(QWidget):
         self.bboxes.append(
             [float(x_min_norm), float(y_min_norm), float(x_max_norm), float(y_max_norm)]
         )
-        self.bbox_meta.append({"color": pen_color, "width": int(width)})
+        self.bbox_meta.append({"color": pen_color, "width": int(width), "label": label})
 
         # Store in all_strokes for consistency
         self.all_strokes.append(
-            {"bbox": bbox, "color": color, "alpha": 128, "width": width}
+            {"bbox": bbox, "color": color, "alpha": 128, "width": width, "label": label}
         )
 
         # Redraw overlay (polylines + all bounding boxes)

src/gui/widgets/image_display_widget.py

@@ -137,7 +137,7 @@ class ImageDisplayWidget(QWidget):
                 height,
                 bytes_per_line,
                 self.current_image.qtimage_format,
-            )
+            ).copy()  # Copy to ensure Qt owns its memory after this scope
 
             # Convert to pixmap
             pixmap = QPixmap.fromImage(qimage)

src/model/inference.py

@@ -5,12 +5,12 @@ Handles detection inference and result storage.
 
 from typing import List, Dict, Optional, Callable
 from pathlib import Path
-from PIL import Image
 import cv2
 import numpy as np
 
 from src.model.yolo_wrapper import YOLOWrapper
 from src.database.db_manager import DatabaseManager
+from src.utils.image import Image
 from src.utils.logger import get_logger
 from src.utils.file_utils import get_relative_path
 
@@ -42,6 +42,7 @@ class InferenceEngine:
         relative_path: str,
         conf: float = 0.25,
         save_to_db: bool = True,
+        repository_root: Optional[str] = None,
     ) -> Dict:
         """
         Detect objects in a single image.
@@ -51,29 +52,42 @@ class InferenceEngine:
             relative_path: Relative path from repository root
             conf: Confidence threshold
             save_to_db: Whether to save results to database
+            repository_root: Base directory used to compute relative_path (if known)
 
         Returns:
             Dictionary with detection results
         """
         try:
+            # Normalize storage path (fall back to absolute path when repo root is unknown)
+            stored_relative_path = relative_path
+            if not repository_root:
+                stored_relative_path = str(Path(image_path).resolve())
+
             # Get image dimensions
-            img = Image.open(image_path)
-            width, height = img.size
-            img.close()
+            img = Image(image_path)
+            width = img.width
+            height = img.height
 
             # Perform detection
             detections = self.yolo.predict(image_path, conf=conf)
 
             # Add/get image in database
             image_id = self.db_manager.get_or_create_image(
-                relative_path=relative_path,
+                relative_path=stored_relative_path,
                 filename=Path(image_path).name,
                 width=width,
                 height=height,
             )
 
-            # Save detections to database
-            if save_to_db and detections:
+            inserted_count = 0
+            deleted_count = 0
+
+            # Save detections to database, replacing any previous results for this image/model
+            if save_to_db:
+                deleted_count = self.db_manager.delete_detections_for_image(
+                    image_id, self.model_id
+                )
+                if detections:
                     detection_records = []
                     for det in detections:
                         # Use normalized bbox from detection
@@ -81,6 +95,15 @@ class InferenceEngine:
                             "bbox_normalized"
                         ]  # [x_min, y_min, x_max, y_max]
 
+                        metadata = {
+                            "class_id": det["class_id"],
+                            "source_path": str(Path(image_path).resolve()),
+                        }
+                        if repository_root:
+                            metadata["repository_root"] = str(
+                                Path(repository_root).resolve()
+                            )
+
                         record = {
                             "image_id": image_id,
                             "model_id": self.model_id,
@@ -88,12 +111,20 @@ class InferenceEngine:
                             "bbox": tuple(bbox_normalized),
                             "confidence": det["confidence"],
                             "segmentation_mask": det.get("segmentation_mask"),
-                        "metadata": {"class_id": det["class_id"]},
+                            "metadata": metadata,
                         }
                         detection_records.append(record)
 
-                self.db_manager.add_detections_batch(detection_records)
-                logger.info(f"Saved {len(detection_records)} detections to database")
+                    inserted_count = self.db_manager.add_detections_batch(
+                        detection_records
+                    )
+                    logger.info(
+                        f"Saved {inserted_count} detections to database (replaced {deleted_count})"
+                    )
+                else:
+                    logger.info(
+                        f"Detection run removed {deleted_count} stale entries but produced no new detections"
+                    )
 
             return {
                 "success": True,
@@ -142,7 +173,12 @@ class InferenceEngine:
             rel_path = get_relative_path(image_path, repository_root)
 
             # Perform detection
-            result = self.detect_single(image_path, rel_path, conf)
+            result = self.detect_single(
+                image_path,
+                rel_path,
+                conf=conf,
+                repository_root=repository_root,
+            )
             results.append(result)
 
             # Update progress

src/model/yolo_wrapper.py

@@ -7,6 +7,9 @@ from ultralytics import YOLO
 from pathlib import Path
 from typing import Optional, List, Dict, Callable, Any
 import torch
+import tempfile
+import os
+from src.utils.image import Image
 from src.utils.logger import get_logger
 
 
@@ -55,6 +58,7 @@ class YOLOWrapper:
         save_dir: str = "data/models",
         name: str = "custom_model",
         resume: bool = False,
+        callbacks: Optional[Dict[str, Callable]] = None,
         **kwargs,
     ) -> Dict[str, Any]:
         """
@@ -69,13 +73,15 @@ class YOLOWrapper:
             save_dir: Directory to save trained model
             name: Name for the training run
             resume: Resume training from last checkpoint
+            callbacks: Optional Ultralytics callback dictionary
             **kwargs: Additional training arguments
 
         Returns:
             Dictionary with training results
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Starting training: {name}")
@@ -117,7 +123,8 @@ class YOLOWrapper:
             Dictionary with validation metrics
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Starting validation on {split} split")
@@ -158,12 +165,15 @@ class YOLOWrapper:
             List of detection dictionaries
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
+
+        prepared_source, cleanup_path = self._prepare_source(source)
 
         try:
             logger.info(f"Running inference on {source}")
             results = self.model.predict(
-                source=source,
+                source=prepared_source,
                 conf=conf,
                 iou=iou,
                 save=save,
@@ -180,6 +190,14 @@ class YOLOWrapper:
         except Exception as e:
             logger.error(f"Error during inference: {e}")
             raise
+        finally:
+            if 0:  # cleanup_path:
+                try:
+                    os.remove(cleanup_path)
+                except OSError as cleanup_error:
+                    logger.warning(
+                        f"Failed to delete temporary RGB image {cleanup_path}: {cleanup_error}"
+                    )
 
     def export(
         self, format: str = "onnx", output_path: Optional[str] = None, **kwargs
@@ -196,7 +214,8 @@ class YOLOWrapper:
             Path to exported model
         """
         if self.model is None:
-            self.load_model()
+            if not self.load_model():
+                raise RuntimeError(f"Failed to load model from {self.model_path}")
 
         try:
             logger.info(f"Exporting model to {format} format")
@@ -208,6 +227,38 @@ class YOLOWrapper:
             logger.error(f"Error exporting model: {e}")
             raise
 
+    def _prepare_source(self, source):
+        """Convert single-channel images to RGB temporarily for inference."""
+        cleanup_path = None
+
+        if isinstance(source, (str, Path)):
+            source_path = Path(source)
+            if source_path.is_file():
+                try:
+                    img_obj = Image(source_path)
+                    pil_img = img_obj.pil_image
+                    if len(pil_img.getbands()) == 1:
+                        rgb_img = img_obj.convert_grayscale_to_rgb_preserve_range()
+                    else:
+                        rgb_img = pil_img.convert("RGB")
+
+                    suffix = source_path.suffix or ".png"
+                    tmp = tempfile.NamedTemporaryFile(suffix=suffix, delete=False)
+                    tmp_path = tmp.name
+                    tmp.close()
+                    rgb_img.save(tmp_path)
+                    cleanup_path = tmp_path
+                    logger.info(
+                        f"Converted image {source_path} to RGB for inference at {tmp_path}"
+                    )
+                    return tmp_path, cleanup_path
+                except Exception as convert_error:
+                    logger.warning(
+                        f"Failed to preprocess {source_path} as RGB, continuing with original file: {convert_error}"
+                    )
+
+        return source, cleanup_path
+
     def _format_training_results(self, results) -> Dict[str, Any]:
         """Format training results into dictionary."""
         try:

src/utils/config_manager.py

@@ -7,6 +7,7 @@ import yaml
 from pathlib import Path
 from typing import Any, Dict, Optional
 from src.utils.logger import get_logger
+from src.utils.image import Image
 
 
 logger = get_logger(__name__)
@@ -46,18 +47,15 @@ class ConfigManager:
             "database": {"path": "data/detections.db"},
             "image_repository": {
                 "base_path": "",
-                "allowed_extensions": [
-                    ".jpg",
-                    ".jpeg",
-                    ".png",
-                    ".tif",
-                    ".tiff",
-                    ".bmp",
-                ],
+                "allowed_extensions": Image.SUPPORTED_EXTENSIONS,
             },
             "models": {
                 "default_base_model": "yolov8s-seg.pt",
                 "models_directory": "data/models",
+                "base_model_choices": [
+                    "yolov8s-seg.pt",
+                    "yolov11s-seg.pt",
+                ],
             },
             "training": {
                 "default_epochs": 100,
@@ -65,6 +63,20 @@ class ConfigManager:
                 "default_imgsz": 640,
                 "default_patience": 50,
                 "default_lr0": 0.01,
+                "two_stage": {
+                    "enabled": False,
+                    "stage1": {
+                        "epochs": 20,
+                        "lr0": 0.0005,
+                        "patience": 10,
+                        "freeze": 10,
+                    },
+                    "stage2": {
+                        "epochs": 150,
+                        "lr0": 0.0003,
+                        "patience": 30,
+                    },
+                },
             },
             "detection": {
                 "default_confidence": 0.25,
@@ -214,5 +226,5 @@ class ConfigManager:
     def get_allowed_extensions(self) -> list:
         """Get list of allowed image file extensions."""
         return self.get(
-            "image_repository.allowed_extensions", [".jpg", ".jpeg", ".png"]
+            "image_repository.allowed_extensions", Image.SUPPORTED_EXTENSIONS
         )

src/utils/file_utils.py

@@ -28,7 +28,9 @@ def get_image_files(
         List of absolute paths to image files
     """
     if allowed_extensions is None:
-        allowed_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        from src.utils.image import Image
+
+        allowed_extensions = Image.SUPPORTED_EXTENSIONS
 
     # Normalize extensions to lowercase
     allowed_extensions = [ext.lower() for ext in allowed_extensions]
@@ -204,7 +206,9 @@ def is_image_file(
         True if file is an image
     """
     if allowed_extensions is None:
-        allowed_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        from src.utils.image import Image
+
+        allowed_extensions = Image.SUPPORTED_EXTENSIONS
 
     extension = Path(file_path).suffix.lower()
     return extension in [ext.lower() for ext in allowed_extensions]

src/utils/image.py

@@ -277,6 +277,38 @@ class Image:
         """
         return self._channels >= 3
 
+    def convert_grayscale_to_rgb_preserve_range(
+        self,
+    ) -> PILImage.Image:
+        """Convert a single-channel PIL image to RGB while preserving dynamic range.
+
+        Returns:
+            PIL Image in RGB mode with intensities normalized to 0-255.
+        """
+        if self._channels == 3:
+            return self.pil_image
+
+        grayscale = self.data
+        if grayscale.ndim == 3:
+            grayscale = grayscale[:, :, 0]
+
+        original_dtype = grayscale.dtype
+        grayscale = grayscale.astype(np.float32)
+
+        if grayscale.size == 0:
+            return PILImage.new("RGB", self.shape, color=(0, 0, 0))
+
+        if np.issubdtype(original_dtype, np.integer):
+            denom = float(max(np.iinfo(original_dtype).max, 1))
+        else:
+            max_val = float(grayscale.max())
+            denom = max(max_val, 1.0)
+
+        grayscale = np.clip(grayscale / denom, 0.0, 1.0)
+        grayscale_u8 = (grayscale * 255.0).round().astype(np.uint8)
+        rgb_arr = np.repeat(grayscale_u8[:, :, None], 3, axis=2)
+        return PILImage.fromarray(rgb_arr, mode="RGB")
+
     def __repr__(self) -> str:
         """String representation of the Image object."""
         return (

src/utils/image_converters.py

@@ -0,0 +1,160 @@
+import numpy as np
+
+from roifile import ImagejRoi
+from tifffile import TiffFile, TiffWriter
+from pathlib import Path
+
+
+class UT:
+    """
+    Docstring for UT
+
+    Operetta files along with rois drawn in ImageJ
+    """
+
+    def __init__(self, roifile_fn: Path, no_labels: bool):
+        self.roifile_fn = roifile_fn
+        print("is file", self.roifile_fn.is_file())
+        self.rois = None
+        if no_labels:
+            self.rois = ImagejRoi.fromfile(self.roifile_fn)
+            self.stem = self.roifile_fn.stem.split("Roi-")[1]
+        else:
+            self.roifile_fn = roifile_fn / roifile_fn.parts[-1]
+            self.stem = self.roifile_fn.stem
+
+            print(self.roifile_fn)
+
+        print(self.stem)
+        self.image, self.image_props = self._load_images()
+
+    def _load_images(self):
+        """Loading sequence of tif files
+        array sequence is CZYX
+        """
+        print("Loading images:", self.roifile_fn.parent, self.stem)
+        fns = list(self.roifile_fn.parent.glob(f"{self.stem.lower()}*.tif*"))
+        stems = [fn.stem.split(self.stem)[-1] for fn in fns]
+        n_ch = len(set([stem.split("-ch")[-1].split("t")[0] for stem in stems]))
+        n_p = len(set([stem.split("-")[0] for stem in stems]))
+        n_t = len(set([stem.split("t")[1] for stem in stems]))
+
+        with TiffFile(fns[0]) as tif:
+            img = tif.asarray()
+            w, h = img.shape
+            dtype = img.dtype
+            self.image_props = {
+                "channels": n_ch,
+                "planes": n_p,
+                "tiles": n_t,
+                "width": w,
+                "height": h,
+                "dtype": dtype,
+            }
+        print("Image props", self.image_props)
+
+        image_stack = np.zeros((n_ch, n_p, w, h), dtype=dtype)
+        for fn in fns:
+            with TiffFile(fn) as tif:
+                img = tif.asarray()
+                stem = fn.stem.split(self.stem)[-1]
+                ch = int(stem.split("-ch")[-1].split("t")[0])
+                p = int(stem.split("-")[0].split("p")[1])
+                t = int(stem.split("t")[1])
+                print(fn.stem, "ch", ch, "p", p, "t", t)
+                image_stack[ch - 1, p - 1] = img
+
+        print(image_stack.shape)
+
+        return image_stack, self.image_props
+
+    @property
+    def width(self):
+        return self.image_props["width"]
+
+    @property
+    def height(self):
+        return self.image_props["height"]
+
+    @property
+    def nchannels(self):
+        return self.image_props["channels"]
+
+    @property
+    def nplanes(self):
+        return self.image_props["planes"]
+
+    def export_rois(
+        self,
+        path: Path,
+        subfolder: str = "labels",
+        class_index: int = 0,
+    ):
+        """Export rois to a file"""
+        with open(path / subfolder / f"{self.stem}.txt", "w") as f:
+            for i, roi in enumerate(self.rois):
+                rc = roi.subpixel_coordinates
+                if rc is None:
+                    print(
+                        f"No coordinates: {self.roifile_fn}, element {i}, out of {len(self.rois)}"
+                    )
+                    continue
+                xmn, ymn = rc.min(axis=0)
+                xmx, ymx = rc.max(axis=0)
+                xc = (xmn + xmx) / 2
+                yc = (ymn + ymx) / 2
+                bw = xmx - xmn
+                bh = ymx - ymn
+                coords = f"{xc/self.width} {yc/self.height} {bw/self.width} {bh/self.height} "
+                for x, y in rc:
+                    coords += f"{x/self.width} {y/self.height} "
+                f.write(f"{class_index} {coords}\n")
+
+        return
+
+    def export_image(
+        self,
+        path: Path,
+        subfolder: str = "images",
+        plane_mode: str = "max projection",
+        channel: int = 0,
+    ):
+        """Export image to a file"""
+
+        if plane_mode == "max projection":
+            self.image = np.max(self.image[channel], axis=0)
+            print(self.image.shape)
+
+        print(path / subfolder / f"{self.stem}.tif")
+        with TiffWriter(path / subfolder / f"{self.stem}.tif") as tif:
+            tif.write(self.image)
+
+
+if __name__ == "__main__":
+    import argparse
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-i", "--input", nargs="*", type=Path)
+    parser.add_argument("-o", "--output", type=Path)
+    parser.add_argument(
+        "--no-labels",
+        action="store_false",
+        help="Source does not have labels, export only images",
+    )
+    args = parser.parse_args()
+
+    for path in args.input:
+        print("Path:", path)
+        if not args.no_labels:
+            print("No labels")
+            ut = UT(path, args.no_labels)
+            ut.export_image(args.output, plane_mode="max projection", channel=0)
+
+        else:
+            for rfn in Path(path).glob("*.zip"):
+                print("Roi FN:", rfn)
+                ut = UT(rfn, args.no_labels)
+                ut.export_rois(args.output, class_index=0)
+                ut.export_image(args.output, plane_mode="max projection", channel=0)
+
+        print()

tests/show_yolo_seg.py

@@ -0,0 +1,184 @@
+#!/usr/bin/env python3
+"""
+show_yolo_seg.py
+
+Usage:
+    python show_yolo_seg.py /path/to/image.jpg /path/to/labels.txt
+
+Supports:
+ - Segmentation polygons: "class x1 y1 x2 y2 ... xn yn"
+ - YOLO bbox lines as fallback: "class x_center y_center width height"
+Coordinates can be normalized [0..1] or absolute pixels (auto-detected).
+"""
+import sys
+import cv2
+import numpy as np
+import matplotlib.pyplot as plt
+import argparse
+from pathlib import Path
+import random
+
+
+def parse_label_line(line):
+    parts = line.strip().split()
+    if not parts:
+        return None
+    cls = int(float(parts[0]))
+    coords = [float(x) for x in parts[1:]]
+    return cls, coords
+
+
+def coords_are_normalized(coords):
+    # If every coordinate is between 0 and 1 (inclusive-ish), assume normalized
+    if not coords:
+        return False
+    return max(coords) <= 1.001
+
+
+def yolo_bbox_to_xyxy(coords, img_w, img_h):
+    # coords: [xc, yc, w, h] normalized or absolute
+    xc, yc, w, h = coords[:4]
+    if max(coords) <= 1.001:
+        xc *= img_w
+        yc *= img_h
+        w *= img_w
+        h *= img_h
+    x1 = int(round(xc - w / 2))
+    y1 = int(round(yc - h / 2))
+    x2 = int(round(xc + w / 2))
+    y2 = int(round(yc + h / 2))
+    return x1, y1, x2, y2
+
+
+def poly_to_pts(coords, img_w, img_h):
+    # coords: [x1 y1 x2 y2 ...] either normalized or absolute
+    if coords_are_normalized(coords[4:]):
+        coords = [
+            coords[i] * (img_w if i % 2 == 0 else img_h) for i in range(len(coords))
+        ]
+    pts = np.array(coords, dtype=np.int32).reshape(-1, 2)
+    return pts
+
+
+def random_color_for_class(cls):
+    random.seed(cls)  # deterministic per class
+    return tuple(int(x) for x in np.array([random.randint(0, 255) for _ in range(3)]))
+
+
+def draw_annotations(img, labels, alpha=0.4, draw_bbox_for_poly=True):
+    # img: BGR numpy array
+    overlay = img.copy()
+    h, w = img.shape[:2]
+    for cls, coords in labels:
+        if not coords:
+            continue
+        # polygon case (>=6 coordinates)
+        if len(coords) >= 6:
+            color = random_color_for_class(cls)
+
+            x1, y1, x2, y2 = yolo_bbox_to_xyxy(coords[:4], w, h)
+            cv2.rectangle(img, (x1, y1), (x2, y2), color, 2)
+
+            pts = poly_to_pts(coords[4:], w, h)
+            # fill on overlay
+            cv2.fillPoly(overlay, [pts], color)
+            # outline on base image
+            cv2.polylines(img, [pts], isClosed=True, color=color, thickness=2)
+            # put class text at first point
+            x, y = int(pts[0, 0]), int(pts[0, 1]) - 6
+            cv2.putText(
+                img,
+                str(cls),
+                (x, max(6, y)),
+                cv2.FONT_HERSHEY_SIMPLEX,
+                0.6,
+                (255, 255, 255),
+                2,
+                cv2.LINE_AA,
+            )
+
+        # YOLO bbox case (4 coords)
+        elif len(coords) == 4:
+            x1, y1, x2, y2 = yolo_bbox_to_xyxy(coords, w, h)
+            color = random_color_for_class(cls)
+            cv2.rectangle(img, (x1, y1), (x2, y2), color, 2)
+            cv2.putText(
+                img,
+                str(cls),
+                (x1, max(6, y1 - 4)),
+                cv2.FONT_HERSHEY_SIMPLEX,
+                0.6,
+                (255, 255, 255),
+                2,
+                cv2.LINE_AA,
+            )
+        else:
+            # Unknown / invalid format, skip
+            continue
+
+    # blend overlay for filled polygons
+    cv2.addWeighted(overlay, alpha, img, 1 - alpha, 0, img)
+    return img
+
+
+def load_labels_file(label_path):
+    labels = []
+    with open(label_path, "r") as f:
+        for raw in f:
+            line = raw.strip()
+            if not line:
+                continue
+            parsed = parse_label_line(line)
+            if parsed:
+                labels.append(parsed)
+    return labels
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description="Show YOLO segmentation / polygon annotations"
+    )
+    parser.add_argument("image", type=str, help="Path to image file")
+    parser.add_argument("labels", type=str, help="Path to YOLO label file (polygons)")
+    parser.add_argument(
+        "--alpha", type=float, default=0.4, help="Polygon fill alpha (0..1)"
+    )
+    parser.add_argument(
+        "--no-bbox", action="store_true", help="Don't draw bounding boxes for polygons"
+    )
+    args = parser.parse_args()
+
+    img_path = Path(args.image)
+    lbl_path = Path(args.labels)
+
+    if not img_path.exists():
+        print("Image not found:", img_path)
+        sys.exit(1)
+    if not lbl_path.exists():
+        print("Label file not found:", lbl_path)
+        sys.exit(1)
+
+    img = cv2.imread(str(img_path), cv2.IMREAD_COLOR)
+    if img is None:
+        print("Could not load image:", img_path)
+        sys.exit(1)
+
+    labels = load_labels_file(str(lbl_path))
+    if not labels:
+        print("No labels parsed from", lbl_path)
+        # continue and just show image
+    out = draw_annotations(
+        img.copy(), labels, alpha=args.alpha, draw_bbox_for_poly=(not args.no_bbox)
+    )
+
+    # Convert BGR -> RGB for matplotlib display
+    out_rgb = cv2.cvtColor(out, cv2.COLOR_BGR2RGB)
+    plt.figure(figsize=(10, 10 * out.shape[0] / out.shape[1]))
+    plt.imshow(out_rgb)
+    plt.axis("off")
+    plt.title(f"{img_path.name} ({lbl_path.name})")
+    plt.show()
+
+
+if __name__ == "__main__":
+    main()

tests/test_image.py

@@ -27,7 +27,7 @@ class TestImage:
 
     def test_supported_extensions(self):
         """Test that supported extensions are correctly defined."""
-        expected_extensions = [".jpg", ".jpeg", ".png", ".tif", ".tiff", ".bmp"]
+        expected_extensions = Image.SUPPORTED_EXTENSIONS
         assert Image.SUPPORTED_EXTENSIONS == expected_extensions
 
     def test_image_properties(self, tmp_path):